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Series GSE24991 Query DataSets for GSE24991
Status Public on Feb 05, 2011
Title [E-MTAB-332] H-NS and Fis binding to E. coli K12
Organism Escherichia coli
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Among the most important regulators of gene expression in bacteria are 'nucleoid-associated proteins'. These proteins alter the topology of the bound DNA by bending, wrapping or bridging it, thus having multiple effects, including transcriptional regulation, on the bacterial cell. Among the best-studied nucleoid proteins are H-NS and Fis, which bind to specific sequences on the DNA. H-NS is a global repressor of gene expression. Fis alters the global conformation of the DNA by introducing branched structures in it; but its effect on gene expression on a genomic scale remains largely unclear. Several bacterial transcriptional regulators including H-NS and Fis have been studied using ChIP-chip. However, the higher resolution and dynamic range offered by ChIP-Seq have not been exploited for any bacterial species. By performing ChIP-Seq of these two proteins, we present the first such study in a bacterium. In addition to providing a proof-of-principle for the use of this technology for bacteria, we perform our study at multiple time-points during growth in rich medium, thus generating new insights into how these proteins function under different cellular conditions. Further, by analysing our data in conjunction with newly-generated gene expression and RNA polymerase-chromosome interaction data we provide new interpretation of the genome-scale patterns of the interactions of these proteins to the DNA.

ArrayExpress Release Date: 2010-07-29

Person Roles: submitter
Person Last Name: Sai Narain Seshasayee
Person First Name: Aswin
Person Mid Initials:
Person Email: aswin@ebi.ac.uk
Person Phone:
Person Address:
Person Affiliation: EBI

 
Overall design Experimental Design: growth_condition_design
Experimental Design: in_vivo_design
Experimental Design: binding_site_identification_design
Experimental Design: ChIP-seq
Experimental Factor Name: IMMUNOPRECIPITATE
Experimental Factor Name: GROWTHCONDITION
Experimental Factor Name: GENOTYPE
Experimental Factor Type: immunoprecipitate
Experimental Factor Type: growth_condition
Experimental Factor Type: genotype
 
Citation(s) 21097887
Submission date Oct 28, 2010
Last update date May 15, 2019
Organization European Bioinformatics Institute
E-mail(s) miamexpress@ebi.ac.uk
Lab ArrayExpress
Street address Wellcome Trust Genome Campus
City Hinxton
State/province Cambridgeshire
ZIP/Postal code CB10 1SD
Country United Kingdom
 
Platforms (1)
GPL10328 Illumina Genome Analyzer II (Escherichia coli)
Samples (9)
GSM613802 [E-MTAB-332] fis early-exponential
GSM613803 [E-MTAB-332] fis mid-exponential
GSM613804 [E-MTAB-332] H-NS early-exponential
Relations
ArrayExpress E-MTAB-332
SRA ERP000280
BioProject PRJNA131971

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE24991_RAW.tar 132.0 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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